Data from: Oscillatory signatures underlie growth regimes in Arabidopsis pollen tubes: computational methods to estimate tip location, periodicity and synchronization in growing cells
Damineli, Daniel S.C., University of Maryland, College Park
Portes, Maria Teresa, University of Maryland, College Park
Feijó, José A., University of Maryland, College Park
Published Apr 04, 2017 on Dryad.
Cite this dataset
Damineli, Daniel S.C.; Portes, Maria Teresa; Feijó, José A. (2017). Data from: Oscillatory signatures underlie growth regimes in Arabidopsis pollen tubes: computational methods to estimate tip location, periodicity and synchronization in growing cells [Dataset]. Dryad. https://doi.org/10.5061/dryad.6806c
Oscillations in pollen tubes have been reported for many cellular processes, including growth, extracellular ion fluxes, and cytosolic ion concentrations. However, there is a shortage of quantitative methods to measure and characterize the different dynamic regimes observed. Herein, a suite of open-source computational methods and original algorithms were integrated into an automated analysis pipeline that we employed to characterize specific oscillatory signatures in pollen tubes of Arabidopsis thaliana (Col-0). Importantly, it enabled us to detect and quantify a Ca2+ spiking behaviour upon growth arrest and synchronized oscillations involving growth, extracellular H+ fluxes, and cytosolic Ca2+, providing the basis for novel hypotheses. Our computational approach includes a new tip detection method with subpixel resolution using linear regression, showing improved ability to detect oscillations when compared to currently available methods. We named this data analysis pipeline ‘Computational Heuristics for Understanding Kymographs and aNalysis of Oscillations Relying on Regression and Improved Statistics’, or CHUKNORRIS. It can integrate diverse data types (imaging, electrophysiology), extract quantitative and time-explicit estimates of oscillatory characteristics from isolated time series (period and amplitude) or pairs (phase relationships and delays), and evaluate their synchronization state. Here, its performance is tested with ratiometric and single channel kymographs, ion flux data, and growth rate analysis.
Ratiometric kymographs of growing pollen tubes
Kymographs of Arabidopsis pollen tubes growing in vitro, featuring two channels (YFP and CFP) of the genetically encoded ratiometric calcium probe YC3.6.
MetaMorph tracking of the pollen tube tip
Tracking and growth rate series of the of the same growing pollen tubes where the ratiometric kymographs where extracted, performed with the 'Track Object' routine in MetaMorph with 3 different ROI sizes.
Synchronized oscillations in growth, H+ flux and intracellular Ca2+
Growth rate series from a tracking software (MetaMorph) is provided, together with a kymograph with fluorescence of a calcium reporter (Yellow Cameleon 3.6) and extracellular H+ flux measurements at the pollen tube tip from an ion-selective vibrating probe. A video with the tracking trace also used as midline to produce the kymograph is also included.
National Science Foundation, Award: MCB-1616437/2016